Functional Nucleic Acid Probes Based on Two-Photon for Biosensing

Functional nucleic acid (FNA) probes have been widely used in environmental monitoring, food analysis, clinical diagnosis, and biological imaging because of their easy synthesis, functional modification, flexible design, and stable properties. However, most FNA probes are designed based on one-photon (OP) in the ultraviolet or visible regions, and the effectiveness of these OP-based FNA probes may be hindered by certain factors, such as their potential for photodamage and limited light tissue penetration. Two-photon (TP) is characterized by the nonlinear absorption of two relatively low-energy photons of near-infrared (NIR) light with the resulting emission of high-energy ultraviolet or visible light. TP-based FNA probes have excellent properties, including lower tissue self-absorption and autofluorescence, reduced photodamage and photobleaching, and higher spatial resolution, making them more advantageous than the conventional OP-based FNA probes in biomedical sensing. In this review, we summarize the recent advances of TP-excited and -activated FNA probes and detail their applications in biomolecular detection. In addition, we also share our views on the highlights and limitations of TP-based FNA probes. The ultimate goal is to provide design approaches for the development of high-performance TP-based FNA probes, thereby promoting their biological applications.

AND-Gated Nanosensor for Imaging of Glutathione and Apyrimidinic Endonuclease 1 in Cells, Animals, and Organoids

The development of a strategy for imaging of glutathione (GSH) and apurinic/apyrimidinic endonuclease 1 (APE1) in an organism remains challenging despite their significance in elaborating the correlated pathophysiological processes. Therefore, in this study, we propose a DNA-based AND-gated nanosensor for fluorescence imaging of the GSH as well as APE1 in living cells, animals, and organoids. The DNA probe is composed of a G-strand and A-strand. The disulfide bond in the G-strand is cleaved through a GSH redox reaction, and the hybridization stability between the G-strand and A-strand is decreased, leading to a conformational change of the A-strand. In the presence of APE1, the apurinic/apyrimidinic (AP) site in the A-strand is digested, producing a fluorescence signal for the correlated imaging of GSH and APE1. This nanosensor enables monitoring of the expression level change of GSH and APE1 in cells. Additionally, we illustrate the capability of this "dual-keys-and-locked" conceptual methodology in achieving specific tumor imaging when GSH and APE1 are present simultaneously (overexpressed GSH and APE1 in tumor cells) with improving tumor-to-normal tissue ratio in vivo. Furthermore, using this nanosensor, the GSH and APE1 also are visualized in organoids that recapitulate the phenotypic and functional traits of the original biological specimens. Overall, this study demonstrates the potential of our proposed biosensing technology in investigating the roles of various biological molecules involved in specific diseases.

Fluorescence-Raman dual-mode quantitative detection and imaging of small-molecule thiols in cell apoptosis with DNA-modified gold nanoflowers

The monitoring of small-molecule thiols (especially glutathione) has attracted widespread attention due to their involvement in numerous physiological processes in living organisms and cells. In this work, a dual-mode nanosensor was designed to detect small-molecule thiols, which is based on the "on-off" switch of fluorescence resonance energy transfer (FRET) and surface-enhanced Raman scattering (SERS). Briefly, DNA was modified by Cy5 (signal probe) and disulfide bonds (recognition element). Gold nanoflowers (AuNFs) were used as the fluorescence-quenching and SERS-enhancing substrate. However, small-molecule thiols can cleave disulfide bonds and release short Cy5-labeled chains, causing the recovery of the fluorescence signal and a decrease of the SERS signal. The nanosensor showed a sensitive response to small-molecule thiols represented by GSH, with a linear range of 0.01-3 mM and a detection limit of 913 nM. In addition, it competed with other related biological interferences and presented good stability and better selectivity towards small-molecule thiols. Most importantly, the developed nanosensor had been successfully applied to in situ imaging and quantitative monitoring of the concentration of small-molecule thiols which changed during T-2 toxin-induced apoptosis in HeLa cells. Meanwhile, nanosensors are also versatile with their potential applications and can be easily extended to the detection and imaging of other human cell lines. The proposed method combines the dual advantages of fluorescence and SERS, which has broad prospects for in situ studies of physiological processes involving small-molecule thiols in biological systems.

Feasibility Study on Facile and One-step Colorimetric Determination of Glutathione by Exploiting Oxidase-like Activity of Fe3O4-MnO2 Nanocomposites

A facile and one-step colorimetric assay is described for the determination of glutathione (GSH). It is based on the use of manganese dioxide-decorated magnetic (Fe₃O₄@MnO₂) nanocomposite that was prepared by an in-situ redox reaction. It exhibits oxidase-mimicking activity and can catalyze the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) without H₂O₂to form a blue colored product (oxTMB) with an absorption maximum at 651 nm. Once GSH is introduced, the component of MnO₂ can be rapidly reduced to Mn²⁺ ions, which leads to inhibit the formation of oxTMB. Based on these findings, a one-step colorimetric assay was developed for the detection GSH in the range of 0.2 to 25 μM with a low detection limit of 0.2 μM without using any procedures of separation and washing. Importantly, the proposed approach is also used to accurately evaluate the intracellular GSH levels. In our perception, the assay is rapid, sensitive and specific.

An ultrasensitive chemiluminescent biosensor for tracing glutathione in human serum using BSA@AuNCs as a peroxidase-mimetic nanozyme on a luminol/artesunate system

In this work, a nanosensor chemiluminescent (CL) probe for sensing glutathione (GSH) was developed, for the first time, based on its inhibition of the intrinsic peroxidase-mimetic effect of BSA@AuNCs. The endoperoxide linkage of artesunate could be hydrolyzed by BSA@AuNCs resulting in the release of reactive oxygen species (ROS), and the consequent generation of strong CL emission. By virtue of the strong covalent interactions of -S⋯Au-, GSH could greatly suppress the peroxidase-mimetic effect of BSA@AuNCs, leading to a drastic CL quenching. The CL quenching efficiency increased proportionally to the logarithm of GSH concentration through the linearity range of 50.0-5000.0 nM with a limit of detection of 5.2 nM. This CL-based strategy for GSH tracing demonstrated the advantages of ultrasensitivity, high selectivity and simplicity. This strategy was successfully utilized to measure GSH levels in human serum with reasonable recovery results of 98.71%, 103.18%, and 101.68%, suggesting that this turn-off CL sensor is a promising candidate for GSH in biological and clinical samples.

Cytidine-gold nanoclusters as peroxidase mimetic for colorimetric detection of glutathione (GSH), glutathione disulfide (GSSG) and glutathione reductase (GR)

Abnormal levels of glutathione (GSH) and glutathione oxidized (GSSG) usually relates to some diseases, thus quantifying the amount of GSH or GSSG is of great significance. A label-free sensing assay based on the enzyme-mimicking property of Cytidine-Au nanoclusters (Cy-AuNCs) was demonstrated for colorimetric detection of GSH, GSSG and glutathione reductase (GR). Firstly, obvious blue color accompanied with an absorption peak at 652 nm was observed due to the high peroxidase-like activity of Cy-AuNCs toward 3,3',5,5'-tetramethylbenzidine (TMB). Then, in the presence of target, the mimetic activity of Cy-AuNCs could be strongly inhibited and used to achieve the visualization detection. The inhibition effect arose from the surface interaction between GSH and Cy-AuNCs. Linear relationships between absorbance response and concentration were obtained between 0 and 0.4 mM for GSH, 0-2.5 mM for GSSG and 0-0.2 U/mL for GR. The limit of detection (LOD) was calculated as low as 0.01 mM, 0.03 mM and 0.003 U/mL for GSH, GSSG and GR, respectively. Furthermore, the proposed method displayed rapid response, easy procedure and high selectivity.

Iodine-Catalyzed Synthesis of N,N'-Chelate Organoboron Aminoquinolate

We disclose a novel method for the synthesis of fluorescent N,N'-chelate organoboron compounds in high efficiency by treatment of aminoquinolates with NaBAr₄/R'COOH in the presence of an iodine catalyst. These compounds display high air and thermal stability. A possible catalytic mechanism based on the results of control experiments has been proposed. Fluorescence quantum yield of 3b is up to 0.79 in dichloromethane.

In situ Analysis of Cancer Cells Based on DNA Signal Amplification and DNA Nanodevices

Cancer is a global disease which has been disturbing researchers in medicine and seriously threatens patients' health and lifetime around the world in the past several decades. Due to the characteristics of cancer cells, such as uncontrollable cell proliferation, cell invasion and metastasis to surrounding tissues, lower grade of differentiation, higher telomerase activity and others, it has been one of the most usual lethal factors, next to heart disease in incidence. Cancer mortality can be decreased by early diagnosis, and the people who with treatment at an early stage have an obvious improved survival rate. Consequently, early detection is significant for better understanding the pathogenesis of cancer and improving the prognosis of patients. In situ detection technique is a vital tool for imaging and cellular pathology research, which can provide effective information about tumor markers in the early cancer detection. In view of low expression of most tumor markers in the early stage of cancers, detection techniques based on DNA signal amplification and DNA nanodevices can provide a strong support for the diagnosis and detection of cancers. In this review, we summarize the research progress of different analytical techniques for detecting various tumor markers that have been reported in recent years. We compare different DNA amplification and nanodevices, then provide guidance and suggestions for better understanding in situ analysis of cancer cells.

Real-Time Visualizing Mitophagy-Specific Viscosity Dynamic by Mitochondria-Anchored Molecular Rotor

Mitophagy, as an evolutionarily conserved cellular process, plays a crucial role in preserving cellular metabolism and physiology. Various microenvironment alterations assigned to mitophagy including pH, polarity, and deregulated biomarkers are increasingly understood. However, mitophagy-specific viscosity dynamic in live cells remains a mystery and needs to be explored. Here, a water-soluble mitochondria-targetable molecular rotor, ethyl-4-[3,6-bis(1-methyl-4-vinylpyridium iodine)-9 H-carbazol-9-yl)] butanoate (BMVC), was exploited as a fluorescent viscosimeter for imaging viscosity variation during mitophagy. This probe contains two positively charged 1-methyl-4-vinylpyridium components as the rotors, whose rotation will be hindered with the increase of environmental viscosity, resulting in enhancement of fluorescence emission. The results demonstrated that this probe operates well in a mitochondrial microenvironment and displays an off-on fluorescence response to viscosity. By virtue of this probe, new discoveries such as the mitochondrial viscosity will increase during mitophagy are elaborated. The real-time visualization of the mitophagy process under nutrient starvation conditions was also proposed and actualized. We expect this probe would be a robust tool in the pathogenic mechanism research of mitochondrial diseases.

A spherical nucleic acid-based two-photon nanoprobe for RNase H activity assay in living cells and tissues

We report here a two-photon nanoprobe for the detection of RNase H activity in living cells and ex vivo tissues by combining a two-photon dye with a spherical nucleic acid (SNA) featuring a DNA/RNA duplex corona and a gold nanoparticle core.

Single-Particle Enzyme Activity Assay with Spectral-Resolved Dark-Field Optical Microscopy

In a clinical assay, enzymes are essential biomarkers for human disease diagnosis. In this work, a spectral-resolved single-particle detection (SPD) method is introduced to quantify alkaline phosphatase (ALP) activity in human serum with a supraparticle (SP) based on MnO₂-modified gold nanoparticle (denoted as GNP@MnO₂ SP) as the probe. In the presence of ALP, 2-phospho-l-ascorbic acid trisodium salt can be hydrolyzed into l-ascorbic acid, which serves as a good reduction agent to trigger the decomposition of the MnO₂ shell on the GNP surface. Given that a trace amount of ALP exists, noticeable scattering color change can be detected at the single-particle level due to the sensitive localized surface plasmon resonance (LSPR) effect from GNPs. With spectral-resolved dark-field optical microscopy, a linear dynamic range of 0.06 to 2.48 mU/mL ( R² = 0.99) and a very low limit of detection of 5.8 μU/mL for the ALP assay are readily achieved, which is more sensitive over the methods based on ensemble sample measurement. As a consequence, this strategy opens a new avenue for the design of an ultrasensitive detection method for disease-correlated biomarker diagnosis in the future.

Color-Coded Single-Particle Pyrophosphate Assay with Dark-Field Optical Microscopy

In this work, we demonstrate a convenient yet sensitive color-coded single-particle detection method for the quantification of pyrophosphate (PPi) by using single gold nanoparticle (GNP) as the probe. The design is based on GNP-dependent catalytic deposition of Cu onto the surface of GNPs with reduced nicotinamide adenine dinucleotide (NADH). Without PPi, Cu²⁺ can be directly reduced to Cu⁰ through the gold-catalyzed oxidization of NADH. In the presence of PPi, the coating process is impeded due to the strong coordination capability of PPi with Cu²⁺. The selective coating of Cu shell onto the GNPs surface results in the extraordinary red-shift of localized surface plasmon resonance from individual GNPs. By quantitatively counting the fraction of yellow particles with color-coded dark-field optical microscopy, the trace amounts of PPi in solution can be accurately quantified. The limit-of-detection is as low as 1.49 nM with a linear dynamic range of 0-4.29 μM, which is much lower than the spectroscopic measurements in bulk solution. In artificial urine sample, good recovery efficiency was achieved. As a consequence, the method demonstrated herein will find promising applications for the ultrasensitive detection of target biomolecules under biological milieu in the future.

An ion quencher operated lamp for multiplexed fluorescent bioassays

A novel and adjustable lamp based on competitive interaction among dsDNA-SYBR Green I (SGI), ion quencher, and analyte was designed for bioanalysis. The "filament" and switch of the lamp could be customized by employing different dsDNA and ion quencher. The poly(AT/TA) dsDNA was successfully screened as the most effective filament of the lamp. Two common ions, Hg²⁺ and Fe³⁺, were selected as the model switch, and the corresponding ligand molecules cysteine (Cys) and pyrophosphate ions (PPi) were selected as the targets. When the fluorescence-quenched dsDNA/SGI-ion complex was introduced into a target-containing system, ions could be bound by competitive molecules and separate from the complex, thereby lighting the lamp. However, no light was observed if the biomolecule could not snatch the metal ions from the complex. Under the optimal conditions, sensitive and selective detection of Cys and PPi was achieved by the lamp, with practical applications in fetal bovine serum and human urine. This ion quencher regulated lamp for fluorescent bioassays is simple in design, fast in operation, and is more convenient than other methods. Significantly, as many molecules could form stable complexes with metal ions selectively, this ion quencher operated lamp has potential for the detection of a wide spectrum of analytes. Graphical abstract A novel and adjustable lamp on the basis of competitive interaction among dsDNA-SYBR Green I, ions quencher and analyte was designed for bioanalysis. The filament and switch of lamp could be customized by employing different dsDNA and ions quencher.

A Target-Lighted dsDNA-Indicator for High-Performance Monitoring of Mercury Pollution and Its Antagonists Screening

As well-known, the excessive discharge of heavy-metal mercury not only destroys the ecological environment, bust also leads to severe damage of human health after ingestion via drinking and bioaccumulation of food chains, and mercury ion (Hg²⁺) is designated as one of most prevalent toxic metal ions in drinking water. Thus, the high-performance monitoring of mercury pollution is necessary. Functional nucleic acids have been widely used as recognition probes in biochemical sensing. In this work, a carbazole derivative, ethyl-4-[3,6-bis(1-methyl-4-vinylpyridium iodine)-9H-carbazol -9-yl)] butanoate (EBCB), has been synthesized and found as a target-lighted DNA fluorescent indicator. As a proof-of-concept, Hg²⁺ detection was carried out based on EBCB and Hg²⁺-mediated conformation transformation of a designed DNA probe. By comparison with conventional nucleic acid indicators, EBCB held excellent advantages, such as minimal background interference and maximal sensitivity. Outstanding detection capabilities were displayed, especially including simple operation (add-and-read manner), ultrarapidity (30 s), and low detection limit (0.82 nM). Furthermore, based on these advantages, the potential for high-performance screening of mercury antagonists was also demonstrated by the fluorescence change of EBCB. Therefore, we believe that this work is meaningful in pollution monitoring, environment restoration and emergency treatment, and may pave a way to apply EBCB as an ideal signal transducer for development of high-performance sensing strategies.

Direct Detection of Nucleic Acid with Minimizing Background and Improving Sensitivity Based on a Conformation-Discriminating Indicator

As is well-known, the nucleic acid indicator-based strategy is one of the major approaches to monitor the nucleic acid hybridization-mediated recognition events in biochemical analysis, displaying obvious advantages including simplicity, low cost, convenience, and generality. However, conventional indicators either hold strong self-fluorescence or can be lighted by both ssDNA and dsDNA, lacking absolute selectivity for a certain conformation, always with high background interference and low sensitivity in sensing; and additional processing (e.g., nanomaterial-mediated background suppression, and enzyme-catalyzed signal amplification) is generally required to improve the detection performance. In this work, a carbazole derivative, EBCB, has been synthesized and screened as a dsDNA-specific fluorescent indicator. Compared with conventional indicators under the same conditions, EBCB displayed a much higher selective coefficient for dsDNA, with little self-fluorescence and negligible effect from ssDNA. Based on its superior capability in DNA conformation-discrimination, high sensitivity with minimizing background interference was demonstrated for direct detection of nucleic acid, and monitoring nucleic acid-based circuitry with good reversibity, resulting in low detection limit and high capability for discriminating base-mismatching. Thus, we expect that this highly specific DNA conformation-discriminating indicator will hold good potential for application in biochemical sensing and molecular logic switching.

Colorimetric detection of glutathione in cells based on peroxidase-like activity of gold nanoclusters: A promising powerful tool for identifying cancer cells

Glutathione (GSH), the most abundant biothiol in cells, not only plays a pivotal role in protective and detoxifying functions of the cell, but also serves as a very important mediator in many cellular functions. Especially, the difference of GSH level between cancer cells and normal cells is regarded as one of most important physiological parameters for cancer diagnosis. It is thereby extremely necessary to develop a simple, sensitive, and reliable analytical method for detection of GSH in cells. On the basis of the inhibition effect of GSH on the peroxidase-like activity of GSH stabilized gold nanoclusters, here a novel and facile strategy for colorimetric detection of cellular GSH level was well established. In this sensing system, GSH can effectively inhibit the oxidation of peroxidase substrate 3,3',5,5'-tetramethylbenzidine (TMB) to produce a blue colored product. Under the optimized conditions, the absorbance at 652 nm against GSH concentration shows a linear relationship within a range from 2 to 25 μM with detection limit of 420 nM. This excellent property allows our approach to be used to accurately evaluate the cellular GSH levels, and it is revealed that the overall GSH level in cancer cells was much higher than that in normal cells. The presented assay will enable a powerful tool for identifying cancer cells in a simple manner for biomedical diagnosis associated with GSH.

Direct Fluorescent Detection of Blood Potassium by Ion-Selective Formation of Intermolecular G-Quadruplex and Ligand Binding

G-quadruplex analogues have been widely used as molecular tools for detection of potassium ion (K(+)). However, interference from a higher concentration of sodium ion (Na(+)), enzymatic degradation of the oligonucleotide, and background absorption and fluorescence of blood samples have all limited the use of G-quadruplex for direct detection of K(+) in blood samples. Here, we reported, for the first time, an intermolecular G-quadruplex-based assay capable of direct fluorescent detection of blood K(+). Increased stringency of intermolecular G-quadruplex formation based on our screened G-rich oligonucleotide (5'-TGAGGGA GGGG-3') provided the necessary selectivity for K(+) against Na(+) at physiological ion level. To increase long-term stability of oligonucleotide in blood, the screened oligonucleotide was modified with an inverted thymine nucleotide whose 3'-terminus was connected to the 3'-terminus of the upstream nucleotide, acting as a blocking group to greatly improve antinuclease stability. Lastly, to avoid interference from background absorption and autofluorescence of blood, a G-quadruplex-binding, two-photon-excited ligand, EBMVC-B, was synthesized and chosen as the fluorescence reporter. Thus, based on selective K(+) ion-induced formation of intermolecular G-quadruplex and EBMVC-B binding, this approach could linearly respond to K(+) from 0.5 to 10 mM, which matches quite well with the physiologically relevant concentration of blood K(+). Moreover, the system was highly selective for K(+) against other metal ions, including Na(+), Ca(2+), Mg(2+), Zn(2+) common in blood. The practical application was demonstrated by direct detection of K(+) from real blood samples by two-photon fluorescence technology. To the best of our knowledge, this is the first attempt to exploit molecular G-quadruplex-based fluorescent sensing for direct assay of blood target. As such, we expect that it will promote the design and practical application of similar DNA-based sensors in complex real systems.

Coupling a DNA–ligand ensemble with Ag cluster formation for the label-free and ratiometric detection of intracellular biothiols

A smart nanoprobe was constructed by coupling a DNA–ligand ensemble with Ag cluster formation for the ratiometric detection of intracellular biothiols.